illumina-strelka

#!/bin/bash


bam="$1"
[[ -z "$1" ]] && { echo "Parameter 1 is empty" 1>&2; exit 1; }
peaks="$2"
[[ -z "$2" ]] && { echo "Parameter 2 is empty" 1>&2; exit 1; }
genome="$3"
[[ -z "$3" ]] && { echo "Parameter 3 is empty" 1>&2; exit 1; }
output_dir="$4"
[[ -z "$4" ]] && { echo "Parameter 4 is empty" 1>&2; exit 1; }
illumina_dir="$6"
[[ -z "$6" ]] && { echo "Parameter 6 is empty" 1>&2; exit 1; }
config="$7"
[[ -z "$7" ]] && { config="configs/configureStrelkaGermlineWorkflow.py.ini" && echo "Path to config file was not specified. Using '$config'." 1>&2; }
if [ ! -f  "$config" ]; then
	echo "The strelka config file ($config) could not be found. Check that it exists." 1>&2; exit 1;
fi
strelka_dir="$8"
if [[ -z "$8" ]]; then
	echo "Strelka directory not specified. Attempting to retrieve from conda env..." 1>&2
	if [[ -z "$CONDA_PREFIX" ]]; then
		echo "Error: not running in conda env" 1>&2; exit 1;
	else
		strelka_dir="$(ls "$CONDA_PREFIX"/share | grep 'strelka' | head -n1)"
		if [[ -z "$strelka_dir" ]]; then
			echo "Error: coudn't find strelka in conda env" 1>&2; exit 1;
		fi
		strelka_dir="$CONDA_PREFIX"/share/"$strelka_dir"
	fi
else
	strelka_dir="$8"
fi
echo "Using strelka dir: $strelka_dir" 1>&2


rm -rf "$output_dir"/results "$output_dir"/workspace "$output_dir"/workflow* "$output_dir"/runWorkflow*

"$strelka_dir"/bin/configureStrelkaGermlineWorkflow.py --bam "$bam" \
--referenceFasta "$genome" --callRegions "$illumina_dir/peaks.bed.gz" \
--runDir "$output_dir" --config "$config" --exome \
--indelCandidates "$illumina_dir"/results/variants/candidateSV.vcf.gz

"$output_dir"/runWorkflow.py -m local && \
bgzip -d "$output_dir"/results/variants/genome.S1.vcf.gz && \
ln -sf results/variants/genome.S1.vcf "$output_dir/illumina-strelka.vcf"